Filename custom option -f with %u, NOT working

[jeodai]

As the title descriped, dcm2niix -f %f_%u ... not working, the result filename is missing acquisition number.

And there is a warning: "Warning: Ignoring '%u' in output filename (recompile to segment by acquisition)".

Anyone knows what happened? Thank you!

[neurolabusc]

This is as intended. As required by the BIDS specification, many modalities stack a range of acquisitions into a single 4D NIfTI file (e.g. fMRI/ASL time series, DTI gradient directions and b-values). Therefore, a single file contains multiple acquisition values (from DICOM tag 0020,0012). For a minimal example, consider this fMRI dataset where two timepoints are acquired: acquisition 1 and 2.

If you want to split a 4D NIfTI file into 3D files, consider a tool like fslsplit.

[jeodai]

This is as intended. As required by the BIDS specification, many modalities stack a range of acquisitions into a single 4D NIfTI file (e.g. fMRI/ASL time series, DTI gradient directions and b-values). Therefore, a single file contains multiple acquisition values (from DICOM tag 0020,0012). For a minimal example, consider this fMRI dataset where two timepoints are acquired: acquisition 1 and 2.

If you want to split a 4D NIfTI file into 3D files, consider a tool like fslsplit.

Thanks for your explanation, I see the consideration.
However I have two small problems:

My test dicom data has no multiple acquisition values, but it is still ignored.
If I want to config it to NOT ignore, do I have to compile the dcm2niix source by myself?

[neurolabusc]

The development branch of dcm2niix will now allow inserting the acquisition number in the filename, though it will generate the warning:

Warning: '%u' in output filename can be misleading (issue 526)

Be aware that this value will not be meaningful for NIfTI files that contain image data from DICOMs with varying acquisition number. While this behavior is now allowed, I would advise against using the -f %u for DICOM to NIfTI conversion, as it was designed for DICOM renaming.

[neurolabusc]

Sorry, added response meant for issue 524. Closing this issue as feature has been added to developmental build.